A New Beginning
by Krazy25
Summary: After 3rd Impact, most believed that everything would go back to normal, but when NERV is being rebuilt, questions arise. What unknown enemy could be lying in the dark.. revised chapter 5 uploaded!
1. Prolgoue

A/N: Thanks to the helpful advice of Roy Batty, I have decided to rewrite my story, same general plot, but I'm going to try and make it better. Please be patient as I try and Improve my writing skills. Thank you!

Disclaimer: I do NOT own Evangelion.

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><p>It had been about 8 months after the tragedy of 3rd Impact, but humanity trudged forward. In such a short time humanity had managed to bounce back once again. City's were being rebuilt at an alarming speed and people were now beginning to go back to the way their lives were before 3rd Impact. For reasons that were unknown to many, NERV was being rebuilt. It had been disbanded for a short period after 3rd impact, but after the amazing recovery of the Evangelion Unit 01, they reformed for an unknown cause. Even though NERV was being rebuilt, it was unknown who the pilots would now be. Many believed that all of the children would refuse to pilot after all they've been through...They were wrong.<p>

_**A New Beginning**_

Shinji didn't know what to do, he thought he was done with NERV after all that had happened, and now, they have the nerve to ask him to pilot EVA Unit 01 again. He didn't know what to do, they wanted an answer by midnight tonight. He was looking forward to a normal life, but piloting EVA was all he knew...What should he do? "_I wonder if Asuka will pilot again..." _Shinji thought to himself as he laid in his hotel bed. After the disband of NERV, he was no longer to be under Misato's care, so he was on his own...again. He remembered seeing Asuka before he left, she didn't say anything to him; she just looked at him with eyes that he could never forget...then he left.

He was lost in his thoughts when his phone rang, "Hello?"

"Shinji?" It was Misato's voice.

"Misato!" He was so glad to hear her voice again.

"How have you been?"

"I'm doing alright...Did they tell you?"

"Yes, I was just calling to let you know...Asuka has agreed to pilot once unit 02 has been fully repaired."

Shinji wasn't all that surprised, piloting EVA was what Asuka worked her whole life for. "Misato...What about Rei? And Toji?"

There was a fairly long pause, "Toji has refused to pilot...and Rei...I'm sorry Shinji...She's gone..."

Shinji figured that they wouldn't be able to find, let alone save, Rei, but it didn't cover up the hurt. After 3rd Impact the first child was no where to be found. "Can I give you a call later with my answer?"

"Yes."

Shinji hung up the phone, he didn't know why, but knowing that Asuka was going to pilot again made him want to pilot too. He didn't know if it was because he had feelings for the bitchy red head or if he just didn't want her to be alone. No one should have to be alone. He sat and thought for several hours, pondering, going back and forth. _"After everything I was put through," _he thought to himself, "_father...I won't do this for you this time..." _thoughts of his father began to anger Shinji, "_How could he have done that to me? Why...I want to know why!.." _

Shinji then began to realize, he didn't care about his father's approval anymore, he didn't have to do anything for him anymore. _"I can get out of his shadow...I am the pilot of Evangelion Unit 01...But this time, I do it for myself!"_

**NERV HQ (Gendo's Office)**

"So the second and third child have agreed to pilot?" Fuyutsuki asked.

"Indeed." Gendo replied. They were in Gendo's office; it was large and open, nothing but a desk inside it. Bare, just like its occupants.

"I figured the third wouldn't."

"That was unexpected as well, but his combat experience will be useful, as for his reliability...that's another subject," Gendo's monotone voice was disturbing.

"Are you going to approve the selection of the Sixth Child?"

"Why wouldn't I? The new unit 03 is already being built."

"Where will this one be coming from?"

"Germany, they've proved efficient in their training of pilots."

Fuyutsuki paused, "Do you have confidence that the third child will be up to the task?"

"That is why we are acquiring the Sixth Child."

"You do not have confidence in the third?"

"No, his past has proved that he is a disobedient child that would be worthless if not for Unit 01," Fuyutsuki was a little taken back by the coldness in Gendo's voice about his own son.

**NERV HQ (Briefing Room)**

Shinji was sitting in a chair at a very long table, this is what used to be a briefing room for when they were fighting Angels. After his decision, he was ordered to be here; he didn't like the room at all, it was bare white, nothing but the table and chairs in it. It made him feel uneasy. Asuka walked through the door, Shinji looked up in sudden excitement, "Asuka!" He ran over and gave the shocked German girl a hug.

"Get off me you dork!" Asuka tried to shove him away, but deep down she was glad to see him too.

"Sorry," Shinji replied as he let go, "Its just been a long time."

"I know, I haven't had a decent meal since you left!"

Shinji smiled, it was nice seeing her again. Misato walked in not too long after, they both were excited to see her and gave her a hug. "Hey you guys," Misato was happy to see the children, they were like her family for so long, she missed them.

"Misato! Do we get to live with you again!" Asuka was eager to know.

Misato smiled, "Yes you do, I've already cleared it with the commander."

It was a happy moment, but things had to get serious sometime. "Alright you two, sit down, I have some documents for you to sign."

Shinji and Asuka sat down, Misato motioned for the Section 2 Agents to bring in the stacks of papers to sign. "Mein Gott!"

"This says that you won't disclose any information about NERV, this is your entry form into NERV, these need to be signed off so you agree to your rank and salary..." Misato went on and on putting paper after paper in front of the children.

**Misato's Apartment**

Shinji walked into Misato's apartment with a box full of his stuff, it was nice to be back here, this is the only place that feels like home. "_I guess Asuka beat me here..." _Shinji thought and sighed at the sight of hundreds of boxes all over the place. Shinji walked into his small room, he smiled, "Its nice to be back."

He unpacked quickly, however, dinner was quickly being demanded by the others. He decided he'd make them a special dish. He was busy cooking when Asuka walked into the kitchen, "Smells amazing, Shinji."

"Thanks," Shinji turned around and said with a slight blush, partly from the compliment and partly from the cleavage he could see from the loose shirt Asuka was wearing.

"What are you looking at?" Asuka screamed. BUSTED.

SMACK. Shinji would now be finishing the meal with a hand print on his face. Misato walked into the kitchen, she noticed the hand print on Shinji's face, "Nice to see everything is back to normal."

They all sat down for there first meal together in a long time, oddly enough, no one really spoke. They simple sat in silence, enjoying each others company. The meal was soon over with and Shinji quickly took care of the dishes. It was time for bed in their new home.

**NERV HQ**

"So it's true..." Gendo studied the satellite images of an enemy target, "We are being faced with a new enemy..."

"With EVA technology," Fuyutsuki stated as he also studied the images.

"We will need to find out more information about this enemy, this enemy EVA may be heading towards us, the satellite was unable to give the location and direction, the transmissions were scrambled upon recording."

"So we are dealing with a organized enemy," Fuyutsuki was unsure of what to make of this.

"Yes, but we will have to wait and see if they will be a threat, these preliminary reports can't be completely trusted, but must be noticed and watched."

"I will designate a team to that purpose," Fuyutsuki paused, "Unit 02 will not be repaired for some time."

"Indeed, it will all be up to the third child; however, if she is threatened, he will do what we want."


	2. Enemy Arise

A/N: Well I hope everyone is enjoying the rewrite, I'll try not to start over again. Enjoy.

Disclaimer: I don't own Evangelion.

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><p>It had been a few days since the two pilots had moved into Misato's apartment. Everything seemed to be back to normal, Asuka and Shinji seemed to get along slightly better than before, though they still had disputes which ended with either a hand print on Shinji's face or a kick in the balls. Misato was putting in a lot of hours, there was still a ton of work that needed to be done on NERV. School wouldn't start back up for the children until next week, they were excused under NERV authority.<p>

The two were in for sync tests today, each concentrating hard during the test. Ritsuko and staff looked over the data on the computers, "Impressive...after all this time they still can hold good scores," Ritsuko recorded some data down.

Misato walked into the room, "How's the test going?"

Ritsuko turned to look at the Major, "Good, Shinji is holding at 78, and Asuka at 72; these scores are amazing after everything that has happened."

Misato was shocked herself at the scores, "That's good news; How is unit 02 coming along?"

"Its approximately 63% repaired, its getting there," Ritsuko replied then opened a COM to the pilots, "Good job, you can go get changed now."

The children were about to do as they were told when the alarms started going off. Everyone looked around in sort of a mix between panic and confusion, then the loudspeakers announced, "First stage alert! Enemy reported heading towards HQ. Pilot Ikari report to unit 01 immediately!"

"You heard the announcement Shinji!" Misato called over the COM, "Eject Shinji now!"

Shinji was ejected from the test plug and rushed his way over to the hangar where unit 01 waited. The entry plug was ready for Shinji when he arrived, he hopped in; the plug was inserted into unit 01. Within a few minutes, unit 01 was activated and moved to the launch ramp where it waited for further instruction. A COM opened up, "Alright Shinji," it was Misato, "The enemy appears to be an EVA, its approaching the outskirts of the city, we're sending you up there unarmed, we don't want to seem hostile and cause a fight if it isn't necessary. If the enemy attacks, however, there will be a positron rifle deployed immediately to your right. Got it?"

"Yes, ma'am," Shinji didn't know if he'd be able to defeat this enemy if it attacked, he didn't know if he had what it took to take another life.

"He looks troubled," Asuka said as she saw Shinji over the COM.

"He does..." Misato agreed with Asuka.

"His heart rate is rising, he's nervous," Ritsuko confirmed.

"Launch Unit 01," Misato ordered hesitantly.

Unit 01 shot up the launch ramp while its pilot prepared himself to do what might needed to be done. When unit 01 reached the surface, he was on the outskirts of Tokyo 3. He turned around and saw the barriers being deployed around the city, he then looked around until he found his target. It was still some ways away, but it was heading right for him. '_I mustn't run away, I mustn't run away...' _He kept repeating this thought through his head as the enemy advanced until it was within shooting distance of Shinji. The enemy stopped dead in its tracks when it spotted Shinji.

Shinji studied his target, it was completely black, its head looked much like unit 00's did. Shinji said over the COM to HQ, "It looks like a prototype."

"It very well may be," the reply came back, it was Ritsuko.

Shinji further studied his target, it looked like it was holding something in its right hand; it looked like a handle for a progressive knife or something. To Shinji's shock, the enemy suddenly started to charge at him, a long blade emerged from the handle almost instantly, "Shit! It's a sword!"

"Deploying rifle!" Misato's voice came over the COM. The grass near Shinji's right foot suddenly opened as a positron rifle shot out, Shinji grabbed it out of the air and aimed. Too late.

The enemy quickly got to him, before Shinji was able to pull the trigger, the enemy's progressive sword sliced clean through the rifle. Shinji tossed the remainder of the rifle aside as the enemy tried to back slash him, he grabbed the enemy's hand. The enemy EVA then tried to throw a punch with his left arm, Shinji managed to grab the fist far before it hit him. Shinji then lifted his right leg and kicked the enemy in the chest, sending him flying back, but he still managed to hold onto the sword.

"Shinji, draw your progressive knife!" Misato ordered over the COM.

"No, if there is a chance, I will take him down without killing him."

"Dammit, Shinji!"

The enemy charged again, Shinji braced himself, it tried to slash Shinji, he dodged to the left of the enemy then land two punches to its head. It tried another backlash, Shinji ducked underneath it and landed two more blows. It then went for a stab at unit 01's waist, Shinji pushed the hand down as it went for the stab then elbowed the enemy in the face. It stumbled back, this was Shinji's chance. He charged at the enemy, shocked, it tried to slash again, Shinji grabbed its hand before it could attack, he grabbed its head with his other hand; the enemy grabbed the hand that was on his head and tried to pull it off, but could not. Shinji then wrapped his leg around the enemies and pulled while pushing the head down, the enemy fell to the ground helplessly. Shinji quickly seized the sword and held it to the throat of the enemy. "You've lost, give up."

Whoops and cheers could be heard over the COM, the enemy EVA looked helpless enough to convince everyone it had given up. Shinji began to walk away, trusting that the enemy pilot knew it was out matched. You shouldn't trust people. Shinji was out of range for hand to hand combat, but the enemy EVA got up drawing its progressive knife. "I told you to give up...I warned you..." Shinji displayed no mercy as he turned around quickly, throwing the progressive sword straight into the chest/core of the enemy EVA. Shinji turned back around and headed towards his retrieval point as the enemy EVA fell to its knees, then to the ground, lifeless.

Shinji was soon back in the hangar, the entry plug ejected, and he hopped out. He was still a little uneasy at what he had just done, but he pulled it together; he was walking towards the changing room when he was stopped by Misato and Asuka. "You kicked its ass, Shinji!" Asuka was actually surprised at how well the third child did.

"Thanks..."

"Why are you so gloomy?" Asuka asked getting really close to his face.

"Asuka, stop," Misato could see that Shinji was upset about what he had done, "You did good Shinji, you have no reason for anyone to tell you otherwise."

Shinji said nothing, he simple walked past them and headed for the dressing room once again. Once he was out of earshot, Asuka asked Misato, "What's up with him?"

"Maybe once you have to take another human life, Asuka, you will understand," Misato said walking off, leaving Asuka.

"Your just going to leave me?" Asuka yelled as she chased after Misato, not really catching what she was just told.

Shinji sat down on the bench in the dressing room, he had changed out of his plug suit and into his normal clothes. He looked at his hands, _'These hands...they took a life..." _That is all that had been running through his mind since he had came off the battlefield. "I gave that pilot a chance," he now said aloud, "Why didn't he take it!" He stood up and slammed his fist into a locker, denting it in. "Shinji," the monotone voice of his father was easily recognized.

Shinji looked up to see Gendo standing in the doorway, "What?"

"You did what you had to do, however, the enemy was not about to abort his objective simply because you told him he lost," What first sounded like Gendo comforting Shinji quickly took the complete opposite feeling, "That was foolish of you to turn your back on an enemy, next time you might not be so lucky to escape with your life."

Shinji wasn't afraid of his father any longer, he clenched his fist in anger rather than self pity, he glared past he father's glasses and into his eyes. Gendo didn't seem effected at all, "If you are going to continue to be on my battlefield you will always keep your eyes on the enemy, if you are defeated your purpose will prove to be useless, understood?"

"Fuck you," Is the only words Shinji could muster up out of his anger.

"Your lucky I need you, otherwise you'd be serving time for insubordination," Gendo left the room.

Shinji punched the locker again, and again, and again; by the time he finished, the locker was clearly going to have to be replaced and his hand was completely numb. He then noticed his knuckles were bleeding quite badly, but as far as he was concerned, he didn't care. He walked around NERV until he found Misato and Asuka. "Where have you been?" Asuka quickly demanded to know.

"Having a conversation with my father," Shinji replied bluntly, Asuka quickly took notice of the blood slightly dripping from Shinji's knuckle.

"Don't tell me, you beat the commander's face in?" Asuka asked.

"I wish..." Shinji simply replied.

"Lets get you to the medical wing," Misato stepped in.

After they got Shinji's hand wrapped up they headed for home, or at least the children thought they were heading home. It was nearly sunset and Misato decided to take a detour to the hilltop where she had taken Shinji after the 3rd Angel. When they arrived both the children didn't understand, they all got out of the car, "What the hell are we doing here?" Asuka asked bluntly.

Shinji hopped the fence and sat on the little piece of land that was on the other side of it, Misato was at first worried but she decided he was fine. Misato and Asuka both decided to join him, Misato sat to his left and Asuka his right. "Its time!" Misato said, a hint of excitement in her voice.

Sirens started to go off as Tokyo 3 began its ascend out of the ground, it was an amazing sight. Shinji was glad Misato took them here, Asuka had never seen this and he was glad he got to see it again. He knew that this was an unspoken message from Misato, saying that he had protected all of this. It was even more beautiful as the sun started to set, Shinji decided to do something he though he would never do. He slid his hand over to Asuka's, and took her hand; Asuka was slightly taken back by the bandaged hand taking hers, but to her own surprise and Shinji's, she didn't pull away. They didn't ever look at each other, they just sat there enjoying the sunset, hand in hand. They knew the evening was over when Misato got up, yawned, and said, "I need a beer."

A/N: Well here is the second revised chapter! Hope you enjoyed Shinji kicking some ass! Gendo, your an asshole! R&R!


	3. Conflicts

A/N: Sorry a little slow on this update, my dog recently had to be put down. R.I.P. Misty Jewel Hawk.

Disclaimer: I don't own Evangelion.

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><p>Shinji was lying in bed, his mind still fluttering with thoughts over what had happened. He wasn't proud at all at what he had done, but for some reason, he felt no grief for the enemy pilot. He couldn't figure out why. Then his thoughts suddenly changed to after the battle, on that hillside; Asuka had let him hold her hand. He didn't know what the red head's intentions were and he was too afraid to confront her about it.<p>

Shinji sighed, "Guess I'll have to wait and find out..."

Over in Asuka's room, she was having similar trouble in finding out the true meaning of what Shinji had done. She looked at her hand, the one he grabbed, _'Why didn't I pull away...' _She thought to herself as she laid in her bed. She was having trouble comprehending the fact that she felt something towards the boy, something she never felt before. She didn't know how to handle this new feeling that was arising inside her, she didn't know what to do about it, and truth be told, it scared her.

**NERV HQ**

There was lots of work to be done on unit 02 in order for it to be battle ready, Commander Ikari did not want to have to face another enemy with only one EVA available. Ritsuko was head of the project, she was in charge of not only getting unit 02 cleared for battle, but to run a full systems check on unit 01 to make sure there were no problems. Ritsuko stood in front of the mostly repaired unit 02, it still needed quite a bit of work on the armor plating around the chest area, but progress is progress. She sighed at the sight of a long night ahead; Unit 02, ordered by Commander Ikari, was to be completed within 48 hours.

**Mistato's Apartment**

Shinji was the first to get up in the house, he starting making breakfast as soon as he got out of the shower. Asuka wasn't long to get up after him, while he was cooking she stumbled out of her room half asleep. "Good Morning," Shinji said without turning around.

"Morning," Asuka mumbled as she made her way to the shower.

PenPen was lured out of Misato's room by the amazing smell of Shinji's cooking, he hopped up onto a chair and waited impatiently for the food. "Morning PenPen," Shinji said as he scraped some food into the penguin's bowl. PenPen simply gave a "Wark!" and then started chowing down.

Shinji had sat down and was quietly eating when Misato walked out of her room, in uniform, to Shinji's surprise. She grabbed a plate of food and sat down next to Shinji, "I got to be at NERV in like 20 minutes," she said between mouths of food, "Oh! You and Asuka have sync tests at 10."

"Alright," Shinji said as he watched his guardian shovel down piles of food and then burst out the door. "Guess I'll handle the mess then," he said to himself as he looked at the messy table with a food covered penguin on it.

"Go take a bath after Asuka gets out," he said to the penguin as he cleaned up. "Wark!" was the reply from PenPen as he waddled into the other room.

A few minutes later Shinji heard Asuka scream, he turned around to see PenPen go flying through the door, then Asuka emerged, only in a towel. PenPen laid on the ground with a foot mark right under his beak, Asuka turned around to see Shinji just standing there. She noticed only a towel was covering her, "What are you looking at?" She said as she kicked Shinji in the face sending him flying into the kitchen sink. "Perverts!" She yelled as she ran back into the bathroom.

PenPen and Shinji laid still for a few minutes, in pain; eventually they got up, slowly, looked at each other, and sighed. Shinji got two ice packs out of the freezer, gave one to PenPen, then sat down on the table with the penguin. Shinji held the ice pack whereas PenPen laid on the icepack on top of the table, they were silently for a short while, then Shinji stated, "It was your fault." "WARK!"

Later that day Shinji and Asuka were at NERV for their tests. Ritsuko looked over the data as Misato looked over her shoulder. "Would you stop hovering!"

"How did they do?" Misato asked backing off.

"Shinji is holding steady at 77 and Asuka is at 74."

"Well at least their scores are staying about the same."

"Agreed," Ritsuko said recording the data, then saying over the COM, "You guys are done, you can get changed and head out."

Shinji and Asuka were walking home when Shinji decided to confront Asuka about what had happened. "Asuka..." she turned to look at him, "On the hillside..." Asuka stopped in her tracks.

"I knew that would come up eventually..." Asuka said looking away.

"Sorry."

"Why are you apologizing? Grow some balls," Asuka said with a hint of emotion seeping through her voice as she quickly starting walking away.

"Asuka."

"What?" She turned around violently.

"I...I..." Shinji couldn't get and words out of his mouth.

"It meant nothing! You thought it meant I liked you, didn't you!" Shinji bowed his head, "I have no use for a spineless wimp of a man! I can't believe I let you grab my hand, that will never happen again! I have no use for a perverted wimp like you so just get out of my life!" Asuka finished shouting as she ran off, tears pouring from her eyes, leaving Shinji.

"I'm sorry..." Shinji didn't know what had just happened, he sat down on the sidewalk, "It was stupid of me to think..." He trailed off into nothingness.

**Misato's Apartment**

Misato got home later that day, she got an uneasy feeling as she walked into the apartment, all the lights were off and she didn't see Shinji or Asuka. She went to Shinji's room, empty; then she decided to try Asuka's room, she found her face down in her mattress. "Everything okay, Asuka?" No answer.

Misato sat down on the mattress next to Asuka, who didn't move. "Asuka what's wrong?"

"Nothing..."

"That's a load a bull," Misato knew something was wrong, "Where is Shinji?"

Asuka looked up at Misato, "I don't know where that dickhead is..."

"Watch your language young lady," Misato sounded like a mother, "Are you two fighting again?"

Asuka was silent once more and Misato's patience was running low, worst of all, she didn't know where Shinji was. Misato was worried even though she knew Section 2 agents most likely had an eye on Shinji. A quick call on her cell phone confirmed it, even though she knew where Shinji was, she still was worried. That boy has been through a lot, again, with the struggling to comprehend the feelings that him and Asuka share, and having to deal with taking another human life, its a lot to put on a teenager.

**NERV HQ**

"There are multiple this time," Fuyutsuki stated as him and Gendo watched a satellite image of two carrier aircraft heading in their direction.

"Two to be exact."

"We are certain they are EVA units?" Fuyutsuki then asked.

"Yes, the MAGI believe that there is a 83.46% chance that it is the same organization that sent the other EVA," Gendo replied.

"How far out?"

"Approximately 1 hour they will be here, who knows what there plan is," Gendo said calmly.

"What about the UN anti-air weapons?" Fuyutsuki asked.

"They will not be in range until the target is approximately 5 minutes away, we are unsure of how effective it will be, my guess is it won't be effective at all," Gendo then opened up a COM to the main deck, "Go to first stage alert." Sirens began sounded throughout the city. "Bring in the children."

**Tokyo 3 Random Bench**

Shinji was sitting on a bench deep in thought when a Section 2 agent approached him. "Sir, we have orders to bring you to HQ," The agent spoke as a car pulled up. Shinji nodded and got inside the car without hesitation. The Section 2 agent pulled out his phone, dialed, then said, "Third child ETA 5 minutes."

**NERV HQ**

Shinji was in the briefing room when Asuka also walked into the room with Misato, no one said a word about what was going on in their personal lives, this was business. Misato was quick to get to the point, "We have two enemy EVA units inbound, unfortunately, Unit 02 is not yet cleared for battle," Asuka was about to object when Misato continued, "They are rushing to try and repair the majority of the chest plate so that it will be able to assist Shinji."

"That's bullshit!" Asuka screamed and slammed her fist on the table.

"Shinji..." Misato looked at the boy who's head was held low, he was already in his plug suit.

"Yes," Shinji looked up slightly at Misato, ignoring the slight peek Asuka had taken at him.

"You will be facing two enemies...alone..." Misato paused as she knew the danger of this situation, "Can you do this?"

"I'm not alone, my mother will be with me," the boy stood up, "Even in death.," he finished and walked out of the room towards Unit 01.

Misato hit the table in anger as she knew Shinji was ready to die in this fight, whatever happened between them two really tore up Shinji's emotions. Misato looked at Asuka who just sat there in her plug suit, letting Shinji walk away, knowing that he could very well die. She couldn't take it anymore, "Dammit Asuka!" Asuka was shocked at Misato's outburst, "I don't give a fuck what happened between you two, but you have to let him know he just can't go out there and die!"

Asuka said nothing, nor did she move. "Asuka!" Misato slammed her fist into the table, she was about to say more when she overheard the intercom, 'Unit 01, launching.'

Misato quickly grabbed a phone, as soon as someone picked up the other end, she began yelling, "Who the hell ordered Unit 01 to launch! I gave no such order!" She paused, "The Commander? What the fuck! Shinji will die!"

Shinji reached the surface soon after, he waiting on the outskirts of the city, the enemy was about to be engaged by anti-air weapons in approximately 1 minute. Shinji was silent in the cockpit of Unit 01, he had a blank expression on his face, emotionless. All too soon, the fire of anti-aircraft guns could be heard for miles. Shinji patiently awaited orders while he watched the bullet fire going into the sky, the two air crafts looked small in the sky.

Under fire, the air crafts made several maneuvers trying to avoid damage, then they made the decision to drop their cargo before they were shot down. Two EVA units dropped out of the planes and free fell towards the Earth. They both activated, these looked pretty much the same as the first, except when they activated, the eye glowed blood red.

**NERV HQ**

"It seems these EVA units have some sort of system similar to the Dummy Plug system of ours!" The report came in.

"Open a COM to Pilot Ikari," Gendo ordered, once the COM opened he continued, "These are Dummy Plug like enemies, meaning they more than likely do not have pilots. Thus, they will be ruthless, destroy them."

**BATTLEFIELD**

Shinji charged rapidly at the falling targets, he was almost in range to take a shot at them with his positron rifle, which was in hand. As soon as he was in range, he opened fire at the targets, the few shots that got near them didn't make it through their AT field. Shinji threw the rifle to the ground and deployed his progressive knife.

The first enemy landed, but Shinji wasn't about to let the other one, he speared the second enemy right out of the sky. The two EVA units plowed into the ground, Shinji got up and spun around just in time to block the other enemy's attack. The enemy pulled out a progressive sword and went for a downward slash, Shinji deflected the slash then spun around and kicked the enemy sending him flying. Shinji barely blocked another sword from the other enemy, who had gotten up, Shinji managed to dodge a couple slashes then grabbed the enemy's hand as he went for another strike, Shinji flipped the enemy's arm around, then kicked it, snapping the enemy's arm backwards. Shinji didn't have a break as the other enemy tackled him to the ground, Shinji managed to kick him off. Shinji got up quickly, dodging and deflecting blows from one enemy, the other one was getting up, he was in trouble.

Shinji was busy with one enemy when the other one swiftly charged at Shinji, he went for a defensive back slash but the enemy dodged it. Before he could react again the enemy had a hold of his arm, which was holding the knife, his attention was distracted for one second when the other enemy went in for a blow. Shinji tried but failed to block the enemy's advance, the enemy EVA stabbed Unit 01 in the stomach while the other one flipped Shinji to the ground causing the sword to rip out the side of Unit 01. Shinji got up quickly, however, as soon as he was up he had two swords at his throat.

A/N: Third chapter is finally completed, hope you liked it, stay tuned to see how this fight ends!


	4. A New Soul Enters

A/N: Well here is chapter 4, I would like to thank all the people that are reading the story. I hope your enjoying it as much as I am.

Incognito girl – I was kind of going for the whole idea Shinji is distracted by Asuka at the moment and he's outmatched 2-to-1. Thank you for your review.

SolidJJ – Thanks for your support, I hope your enjoying the story!

Disclaimer: I do NOT own Evangelion!

Shinji didn't know what happened, one minute he was fighting the two enemy EVA units, and then the next moment here he was in a hospital bed. The room was all pale white which gave an uncomfortable feeling to it. His head was pounding with pain, he soon realized he also had a neck brace on, _'What happened...'_ he thought to himself.

**48 hours earlier...**

"SHINJI!" Misato yelled over the COM at the sight of Unit 01 falling to the ground, head nearly decapitated, "Convert all power to life support! Pilot safety is our top priority!"

Shinji laid inside Unit 01, he was intense pain around his neck, he didn't know what to do next. He had lost; he failed everyone. He didn't want to die, he wasn't ready to die yet, death came even closer as he saw the two enemy's approaching him once again. "I don't want to die..." Shinji muttered to himself as he blacked out.

"Fire all UN weapons, lead the enemies away from Shinji!" Misato ordered.

Missiles and gunfire lit up the sky in an effort to save the young boy that was trapped inside Unit 01. The two enemy EVA units were not affected at all be the weapons, but to Misato's relief, they concentrated on destroying the UN weapons and let Shinji be, at least for now.

Suddenly, Gendo spoke up, "Unit 03 is inbound, ETA 2 minutes."

"What?" Misato whipped around and looked at the Commander.

"Unit 03 will be deployed immediately from its aerial carrier, it is equipped with a positron rifle, only a single round, and a progressive knife," Gendo informed.

"Your sending an inexperienced pilot to fight two enemies alone! How many more pilots have to die?" Misato was outraged.

"As many as it takes."

Misato couldn't believe the coldness in her own commanding officer, she then looked at Ritsuko, "Unit 02?"

"Asuka is ready to go...but sending Unit 02 out at this point will cause more harm than good, the front chest plate is still not properly in place. It will be at least an hour."

"Dammit..." Misato couldn't stand the thought of not only Shinji dying, but this poor new pilot with no combat experience being thrown into battle that he will lose.

Misato knew she didn't have a lot of time before the UN weapons would all be destroyed and the two enemies would go back for Shinji. "Could we have Asuka in Unit 02 attack from long range?"

"If they charge her she would most likely die, there is only a minimum layer of chest armor on Unit 02 right now," Ritsuko replied with no faith in Misato's plan.

"What if Unit 02 attacks from long range while Unit 03 is in the midst of its aerial dive assault on the enemies?" Misato was forming a plan in her mind.

"The risks are too high," Ritsuko replied bluntly.

"So the risks of sending one inexperienced pilot in to face two enemies by his lonesome is better?" Misato confronted Ritsuko.

Ritsuko said nothing. Misato then looked up at the Commander whom she knew was listening to her plan, he gave a slight nod in approval. "Alright, deploy Unit 02 in Sector 862-77, that should be far enough away from the battlefield. Make sure the positron sniper rifle is deployed there as well," she then opened a COM to Unit 02, with Asuka inside, and explained her plan.

Asuka, being her cocky self, complained, "I don't know why you don't have faith in me to take these two out! Just cause Shinji lost doesn't mean I will!"

"Asuka...one blow near the chest, whether it be a sword or fist, would most definitely harm or even kill you. That is how weak your armor is at this point," Misato waited a couple seconds with no response, "Good, you understand."

"Yes, ma'am..." Asuka replied, defeated.

"Unit 02 and positron sniper rifle have been successfully deployed to sector 862-77," a technician reported.

"Now we have to wait for Unit 03, has the pilot been notified of the plan?" Misato was not allowed contact with the new pilot do to some international issues.

"Yes, Unit 03 pilot has been informed of the plan, ETA 1 minute until drop," was the report from the pilot of the carrier.

"There going after Shinji!" Ritsuko shouted in horror as she watched the two enemy EVAs, after destroying most of the UN weapons, start heading back to finish Shinji off.

"Dammit!" Misato could do nothing but watch as they picked unit 01 up, "Shinji defend yourself!"

Shinji was still blacked out, but the pulsating pain was enough to wake him back up as Unit 01's head was ripped clean off. Shinji's screams filled the monitors as the enemy EVAs ripped at Unit 01, they were about to tear off an arm when a clean shot through the head of one of the enemy units stopped them. They quickly traced where the shot had came from, Unit 02.

The two enemy EVA units charged onto unit 02's position, she fired again clipping the shoulder of the other enemy. Without any hesitation the enemy's still charged, Asuka was quite far away so she had a couple more shots before they reached her. She fired, miss. "Dammit!" Asuka cursed as she cocked the bolt action rifle. She was panicked, not taking her time, she fired; miss.

Suddenly Unit 03 appeared, free falling, from above the clouds; gun in hand. He fired onto the two enemy's position, being a rifle and long range, it wasn't accurate, at all. This was enough, however, to stop the charge on Asuka, the enemy's stopped cold, confused, not knowing what to do next. Asuka took the chance to fire again, she hit this time; clean through the shoulder of the enemy she shot in the head. The two enemy's made up there battle plan quickly, the mostly injured one charged Asuka, swaying back and forth making hitting it near impossible; the other, charged towards Unit 03.

The enemy was getting closer and closer to Asuka, she had to make a shot soon, otherwise, it could be really bad. She lined up her sights, trying to keep calm, she fired...miss; "Scheiste!" she cursed as the enemy leaped towards her. She quickly cocked the bolt action and lifted the barrel up stabbing the leaping enemy in the chest with it, the force from the impact knocking her on her back. "Fuck you!" She yelled and fired the gun sending the bullet straight through the enemy's chest, it groaned, she cocked the gun once more, "DIE!" she yelled as she shot again. The enemy EVA fell backwards, landing on its back, silent.

Unit 03 was caught off guard when he was tackled as soon as he landed, he struggled around on the ground with his enemy. This was his first real battle ever, and he was terrified; fear drove him to ward off his attacker. The enemy EVA was on top of him, wailing on him, like an ape on a small child, it started ripping at his arm when he managed to shove it off. A COM opened up to a red head girl, "Get that thing in a clean line of sight and I'll take care of it." The boy said nothing, only nodded, he tried to attack the enemy, but his lack of experience got the better of him. He charged blindly at the enemy, the enemy countered by side stepping and punching him in the back of the head, sending him to the ground. The enemy was once again on top of him, holding him down, he managed to free an arm, he punched the enemy EVA, trying to get him off the top of him. The enemy EVA got a hold of his arm once again, pinning him down, roaring like an animal.

A bullet out of no where tore through the enemy's skull, causing him to lean back slightly, Unit 03 shoved the enemy off him. He quickly grabbed the enemy by the throat, held him up to the side of Unit 03, a clear shot for the red head. Moments later, a bullet pierced the core of the enemy EVA, killing it; he ran out of power seconds later.

**Present Time...**

Shinji still didn't know exactly what happened, he was surprised, however, when Asuka stopped by to see him. She walked into the room wearing a red sun dress, "How are you doing, idiot?" She asked sitting down in a chair against the wall.

"Fine..." Shinji still had an uneasy feeling about what had happened between them.

"Lets get things straight, I'm only here because Misato wanted me to be here, got it?" Asuka said defensively.

"Right.." He mumbled as a nurse came in and checked some things.

"When will you be out?" Asuka asked trying not to show concern in her voice.

The nurse answered for him, "He should be out shortly, actually."

"Thank you," the red head replied as the nurse left, "about time, you've been in here for two days."

"Really?" Shinji wasn't aware of this and was shocked at first.

"Yeah, and you haven't met the new pilot either," Asuka sat up in her chair.

"New pilot?"

"Yeah, he's the one that helped me save your ass, even though I did most of the work," Asuka seemed intent on not letting Shinji live it down that he needed her help, he was going to be hearing about this for a while.

Shinji was about to say something, but stopped when he saw Misato walk in with a boy about his age with her. "How are you, Shinji?" Misato asked.

"Good I guess."

SMACK! Shinji didn't really seemed fazed by the red hand print left on his face. "That's for being inconsiderate of the danger you put yourself into."

"Sorry..."

"Always apologizing..." Asuka mumbled to herself.

After a brief pause, Shinji asked, "Is that the new pilot?"

"Yes, the name's Kai," the boy reached out to shake Shinji's hand.

Shinji shook his hand, he quickly looked over his new teammate; he was about the same height as Shinji, fairly good build, had blonde hair and blue eyes. "Pleased to meet you," Shinji replied.

(A/N: I am in no way referencing Kai to Adolf Hitler and all that Aryan race stuff)

"He's German!" Asuka said with a bit of pride in her voice.

"Anyway," Misato decided to change the subject, "We just got your release forms, so you need to get changed and we can all go out to dinner, sound good?"

"Yeah," Shinji didn't realize how hungry he was.

Kai and Asuka were the first two to walk out the door, Shinji stopped Misato, "Hey Misato, did you tell Asuka to come check on me?"

"No, why?" Misato looked a little puzzled.

"No reason..." Shinji's words trailed off.

Misato looked at the confusion emerging in the young boy's eyes, she walked back over to where the boy sat on the hospital bed, "I don't know what happened between you two, but you'll get through it, relationships just don't start all of a sudden, it takes work, ya know?"

"Relationship?" Shinji was a little shocked at what Misato was saying and was red all over.

"Shinji...I've seen the way you two are together, its only a matter of time," Misato decided to end it now before they got too in depth, "Get dressed, I'm hungry!" She finished patting Shinji on the back.

"Alright," Shinji seemed a bit more cheery but was still confused about how to approach Asuka.

They went to a small restaurant not far from Misato's apartment, it was a nice, not to mention cheap, sit down restaurant. The four sat down, taking note Shinji sat by Asuka, and looked over the menu to try and decide what to eat. After a few minutes, they all decided and ordered some food. "So Kai, you're from Germany?" Shinji decided to spark up a conversation with the new pilot.

"Yes," Kai took a sip of water, "I grew up there my entire life, but I have been studying Japanese since I could talk."

"Well I would like to thank you, and Asuka," Shinji sad catching the two a little off guard.

"You mean for saving your sorry ass?" Asuka quickly covered up her emotions as she looked away from Shinji.

"Yes, thank you," Shinji didn't take any notice to Asuka trying to blow him off.

"Your welcome, Shinji, but I was only protecting a teammate," Kai raised his glass to Shinji, "After all, you are the savior of mankind."

Shinji blushed slightly at the compliment, he didn't exactly like being called the savior of mankind, but he didn't mind it either; it made him feel useful. Asuka said nothing to neither praise Shinji nor insult him. There food came shortly after this; they each ate with smiles across their faces at the delicious food. They all cleaned their plates and were ready for a good night's rest. Kai, however, was stationed to stay in the apartments at NERV HQ. "I guess I will see you guys later," Kai said as they walked outside the restaurant.

"You going to make it home alright?" Misato asked, sounding more and more like a mother.

"Yes ma'am, Thank you for the dinner by the way, it was delicious."

"Your very welcome, you all deserved it," Misato looked at all the children.

They went there separate ways from here, Kai headed back to his apartment at NERV HQ, where as the trio headed towards Misato's apartment where a hungry penguin awaited for any leftovers, he would be disappointed.

A/N: Sorry about the slow update, been a little busy, I'll try and keep it at least weekly! I was actually debating on whether or not to bring in the new pilot, but I remembered I referenced his coming in earlier chapters so I had to bring him in. I'll try my best to make him fit in perfectly! To anyone's question, Shinji and Asuka WILL remain main characters. Thanks for reading!


	5. I'll always be here for you

A/N: I am terribly sorry about the really really delayed update, first year of college and starting a new job kicked my ass pretty bad. I have decided to redo Chapter 5 completely because it was rushed and well...I didn't like it. Thank you all once again for reading, enjoy.

Disclaimer: I do not own Evangelion...unfortunately

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><p><strong>Commander Ikari's Office<strong>

Fuyutsuki sat across from the commander, "This new arising threat is...intriguing."

"Indeed," Gendo replied looking over several sheets of reports, images, etc.

"How are they remaining off the grid?" Fuyutsuki studied one report as Gendo looked at another.

"That is the important question. For them to be able to remain this discrete after amounting two attacks is truly puzzling; they must have strong allies that are protecting them," Gendo's monotone voice showed signs of distress.

Fuyutsuki nodded in agreement, "They must have wealthy investors as well."

"Indeed," Gendo held the images of the three EVA's that had attacked previously, "After serious investigations into the enemy EVA's, it would appear that the assumption is they are prototypes."

Fuyutsuki sighed deeply, "I presume that we can assume that our enemy did not intend to win those battles?"

Gendo placed the images down, "Correct, they were not only testing their prototypes, but I believe they were testing our defenses as well."

**Misato's Apartment**

Shinji was up early making breakfast and lunch boxes, it was going to be there first day of school since who knows when. Wanting to get off on the right foot with the new pilot, he decided to make three lunch boxes. Asuka was a bit late to get up as she rushed out of her room and into the shower, kicking the penguin out mid-shower. Flustered, PenPen retreated to his fridge.

Things between Asuka and Shinji weren't appearing to become any better, they hardly spoke to each other anymore; Shinji didn't really know what to do, he wanted to make things right with Asuka, but why should he when all she does is give hurt in return? He was distressed to the point where he actually asked Misato for advice last night.

**Night Before...**

Misato had a mothering look as she spoke to him, "Shinji, you two have been through a lot together. Throughout everything you two have remained friends," she thought a moment, "or whatever you guys are," Shinji blushed, "You are both at a stage in your life where a lot of things don't make sense, but believe me, you'll figure it out."

Shinji then asked her, "What did you mean before," he looked down, "when you said it's only a matter of time?"

Misato smiled as she stood up, "I just have a feeling about you two," she then headed to bed thinking to herself, '_and I got that bet with PenPen...'_

**Present**

All in all, Shinji didn't really seem to find Misato's advice helpful to the situation he was in now. The lunches were all packed up, breakfast was served, and Shinji could finally sit down and enjoy the first meal of the day. Soon after, Misato joined him, then the red head. Like most of the meals lately, the only talking was replies to Misato from the children; even then they were short replies. Misato couldn't help but feel bad for the two, they have been through so much together yet they can't even have a conversation over breakfast.

Not long after, Kai arrived at the apartment to join up with the other two before leaving for school. The walk to school wasn't very talkative either, though Kai barely knew either of them he could definitely feel the tension in the air. Shinji could notice the uncomfortable look on Kai's face as they walked down the sidewalk, so he decided to break the silence, "Are you settling into your new apartment, Kai?"

Kai appreciated the attempt, "Yeah, though I am having trouble finding my way around NERV."

"Oh, well after school today I'll come over and try to help you out," Shinji said with a smile.

Kai was grateful for his new friend's offer, "Thank you, that would be great," he then looked at the red head who was fairly far up from him and Shinji. _'I wonder what happened...' _he thought to himself.

School proved to move along even slower than it did before, Shinji found himself barely able to keep his head up as he stared at the clock, waiting for lunch. His eye was then drawn to Asuka, who sat a row over and several seats in front of him, she was looking downward and her face suggested she was spacing out, big time. She then noticed Shinji was staring at her, she tilted her head slightly back to look at him, it was the first time their eyes had met in several days.

Lunch had finally arrived, the only contact that Asuka and Shinji made with each other was when he gave her the box lunch. Kai sat down next to Shinji who presented him with a box lunch, he was shocked to see Shinji's generosity. "Thank you, Shinji," He spoke to the third child.

Toji and Kensuke joined the two a few moments later, introductions were made, then they all decided to enjoy some food. "So Kai," Toji spoke between mouthfuls, "your the new pilot then?" Kai nodded, "I guess you can blame me for that one."

"It's hardly the fault of yourself," Kai took a drink, "I've been training to pilot EVA for the majority of my life, I'm sure my services would have been called upon regardless of your decision."

Tears began streaming down Kensuke's face, "I don't know how Toji could pass up that opportunity!"

Toji looked over at Kensuke, "It's not as glorious as you think, is it Shinji?"

Shinji had been staring out the window, the sudden address snapped him back in to reality, "Uh yeah, I mean especially against this new enemy."

"That's for sure, I know I got my ass kicked," Kai poked around at his food as he remembered getting beaten up before Asuka took the killing blow.

"Could be worse!" Kensuke pointed out, "At least you didn't get trapped inside an angel controlled EVA or get your eye blown out of your skull." Both Shinji and Toji held there heads low as if they were reliving those past moments.

"I heard about the situation with EVA unit 03, it was tragic," Kai tried to speak lightly around Shinji and Toji.

"Can we change the subject?" Toji asked looking away.

"Of course," Kai didn't want to push the subject.

All too soon lunch was over with, and the second part of the school day seemed to drag on longer than the first. Finally, the bell sounded for the day to end; Shinji spent the majority of the second half of school thinking about whether to confront Asuka or not. He had made his decision, he walked over to Toji, Kensuke, and Kai; "Toji, Kensuke, can you guys go with Kai back to his apartment, I'll be there shortly, there's just..." Shinji didn't know how to say it as Asuka caught his eye as she was leaving.

"Understood," Toji replied as he patted Shinji on the back, "Good luck my man," him and Kensuke then started to leave.

"I'll be there as soon I can, Kai."

"Do what you need to do to make things right, my friend; there is always another day for a tour," Kai said with a smile.

"Thank you," Shinji smiled as well as Kai left with the other two.

Shinji wasn't sure where Asuka was going, but it sure wasn't home. He caught up with her in a park, she was sitting down on a bench with a blank stare on her face. He swallowed hard as he gathered up the courage to approach her; he then walked up and sat down next to her.

"You followed me?" Asuka asked not taking her eyes off the ground.

"Yes, I want to talk to you."

"Why?" Asuka asked, not making eye contact.

Shinji didn't really think this one through, he figured he would of figured out something to say by the time he got here, but now that he is here, he can't find words. Shinji took a deep breath, "I wanted...to apologize."

This caught Asuka's attention, her head moving up slightly, she looked dead into Shinji's eyes, "For what?"

Shinji stared back into her's, confusion and hurt were dancing around in the young girl's eyes. "After all this time," Shinji looked up at the beautiful blue sky, taking another breath, "I should of known not to approach you so abruptly. So I am sorry that I threw that sort of burden on you so suddenly. It was wrong of me."

His words seemed to linger in the air for quite sometime, then, "No."

Shinji looked once again at Asuka, "No?"

It was then Asuka's turn to take an incredibly deep breath, "I was wrong," Shinji couldn't seem to comprehend those three words coming from her mouth, but listened as she slowly continued, "This isn't going to be easy for me," she took a couple more deep breaths.

"You don't have-"

"Yes I do," she cut Shinji off, after a short pause, she continued, "I...I am sorry, Shinji. I lashed out at you...I didn't mean to..I mean your my...my friend," Shinji looked at the red head as she was nearly in tears, "I'm...I'm so sorry."

She couldn't hold back the tears anymore, her hands covered her face as the tears ran down her cheeks. "Asuka..." Shinji tried to put a comforting hand around the German, "It's okay."

"How can you say that?" her teared filled eyes looked up at Shinji.

Shinji was fighting to hold back tears of his own, "Because...Asuka...That's what friends do," she went back to looking at the ground, "they forgive each other."

After what seemed like a long pause, Asuka managed to wipe away the tears, "...You consider me to be your friend?...After everything?"

Shinji smiled, "Yes, Asuka."

Asuka let a slight smile escape her lips as well, "Thank you..." the smile faded, "you know..I've never really opened up to anyone before.."

"Well," Shinji paused a moment, gathering words, "I'll always be here for you, I promise."

Asuka really didn't have a reply for that, and Shinji didn't really expect one. Shinji decided it was time to remove his arm from around the German girl. He was glad everything was working out between him and Asuka, he didn't tell her, but in all honesty, she was his best friend.

"Can we keep this between you and I?" Asuka asked as the two stood up.

"Of course."

"And another thing..." Asuka let a slight blush come across her face, "This is the ONLY time I am going to do this, understand?"

Shinji was a bit confused, but nodded in agreement; Asuka then approached him, wrapped her hands around him, and pulled him in for a hug. After a few moments of pure shock, Shinji returned the hug. "Thank you for everything, Shinji."

"Your welcome, Asuka."

"This doesn't mean I'm going to change the way I treat you," Asuka said as the hug ended.

"I wouldn't want it any other way," Shinji replied with a smile.

Asuka breathed a deep sigh of relief, "Well, now that we got this straightened out, what do you say we go catch up with Kai and the others?"

"Sure," Shinji was glad everything worked out as well, but then he wondering, "Asuka, how did you-"

"I overheard you idiots, you talk so damn loud," she cut him off as they headed towards Kai's apartment.

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><p>AN: There you have it, the revised Chapter 5. Not a lot of action but some clearing of the feelings between Shinji and Asuka. But is what they have truly friendship, or something more? Guess you'll have to read and find out! Hope you enjoyed it!


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